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Entry version 89 (12 Aug 2020)
Sequence version 1 (01 Mar 2002)
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Protein

Coproheme decarboxylase

Gene

chdC

Organism
Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in coproporphyrin-dependent heme b biosynthesis (PubMed:27758026, PubMed:31423350). Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway (PubMed:27758026, PubMed:31423350, PubMed:29536725). The reaction occurs in a stepwise manner with a three-propionate intermediate (PubMed:27758026, PubMed:31423350).3 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Fe-coproporphyrin IIIUniRule annotation1 PublicationNote: Fe-coproporphyrin III acts as both substrate and redox cofactor (PubMed:27758026). Was originally thought to use heme as a cofactor (PubMed:25602700).2 Publications

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

  1. KM=37.1 µM for H2O21 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: protoheme biosynthesis

    This protein is involved in the pathway protoheme biosynthesis, which is part of Porphyrin-containing compound metabolism.UniRule annotation1 Publication
    View all proteins of this organism that are known to be involved in the pathway protoheme biosynthesis and in Porphyrin-containing compound metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei133Fe-coproporphyrin IIIUniRule annotationCombined sources1 Publication1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei147UniRule annotation1 Publication1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi174Iron (Fe-coproporphyrin III axial ligand)UniRule annotationCombined sources1 Publication1
    Binding sitei187Fe-coproporphyrin IIIUniRule annotationCombined sources1 Publication1
    Binding sitei225Fe-coproporphyrin IIIUniRule annotationCombined sources1 Publication1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionOxidoreductase
    Biological processHeme biosynthesis
    LigandHeme, Iron, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    LMON169963:LMO2113-MONOMER

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00252

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Coproheme decarboxylase1 PublicationUniRule annotation (EC:1.3.98.5UniRule annotation3 Publications)
    Alternative name(s):
    Coproheme III oxidative decarboxylaseUniRule annotationCurated
    Hydrogen peroxide-dependent heme synthaseUniRule annotationCurated
    LmCld1 Publication
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:chdC1 PublicationUniRule annotation
    Synonyms:hemQ1 Publication
    Ordered Locus Names:lmo2113
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiListeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri169963 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesListeriaceaeListeria
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000817 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi147Y → A or H: Loss of activity. 1 Publication1
    Mutagenesisi149M → A: Slight decrease in activity. 1 Publication1
    Mutagenesisi187Q → A: Alters Fe-coproporphyrin III binding. Does not affect kcat, but the reaction is less efficient and a higher excess of hydrogen peroxide is needed. 1 Publication1

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002940421 – 251Coproheme decarboxylaseAdd BLAST251

    Proteomic databases

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    Q8Y5F1

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homopentamer (PubMed:25602700, PubMed:27758026, PubMed:31423350). Homohexamer in solution (PubMed:25602700).

    3 Publications

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    169963.lmo2113

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1251
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    Q8Y5F1

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni147 – 151Fe-coproporphyrin III bindingUniRule annotationCombined sources1 Publication5

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the ChdC family. Type 1 subfamily.UniRule annotationCurated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG3253, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_063226_1_0_9

    KEGG Orthology (KO)

    More...
    KOi
    K00435

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    RYTMWSV

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    Q8Y5F1

    Family and domain databases

    HAMAP database of protein families

    More...
    HAMAPi
    MF_01442, Coproheme_decarbox_1, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR011008, Dimeric_a/b-barrel
    IPR010644, Put_peroxidase/dismutase
    IPR031332, UPF0447

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR36843, PTHR36843, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF06778, Chlor_dismutase, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF54909, SSF54909, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    Q8Y5F1-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MNEAVKTLDG WFCLHDFRSI DWAAWRELNP GNQELMLNEL SHFLSDMEIT
    60 70 80 90 100
    KNIGEGEHTI YSILGQKADL VFFTLRDSLE ALNEVENRFN KLAIADYLLP
    110 120 130 140 150
    TYSYISVVEL SNYLASHMAG GDDPYQNKGV RARLYPALPP KKHICFYPMS
    160 170 180 190 200
    KKRDGADNWY MLPMEERQQL IRDHGLIGRS YAGKVQQIIG GSIGFDDYEW
    210 220 230 240 250
    GVTLFSDDAL EFKRIVTEMR FDEASARYAE FGSFFIGNLL LSEQLSKLFT

    I
    Length:251
    Mass (Da):28,852
    Last modified:March 1, 2002 - v1
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iD355A6F544402061
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    AL591982 Genomic DNA Translation: CAD00191.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    AI1338

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_465637.1, NC_003210.1
    WP_003722373.1, NZ_CP023861.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CAD00191; CAD00191; CAD00191

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    47225563
    984744

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    lmo:lmo2113

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|169963.11.peg.2165

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL591982 Genomic DNA Translation: CAD00191.1
    PIRiAI1338
    RefSeqiNP_465637.1, NC_003210.1
    WP_003722373.1, NZ_CP023861.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4WWSX-ray2.00A/B/C/D/E1-251[»]
    5LOQX-ray1.69A/B/C/D/E2-251[»]
    6FXJX-ray1.79A/B/C/D/E1-251[»]
    6FXQX-ray1.69A/B/C/D/E2-251[»]
    SMRiQ8Y5F1
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi169963.lmo2113

    Proteomic databases

    PaxDbiQ8Y5F1

    Genome annotation databases

    EnsemblBacteriaiCAD00191; CAD00191; CAD00191
    GeneIDi47225563
    984744
    KEGGilmo:lmo2113
    PATRICifig|169963.11.peg.2165

    Phylogenomic databases

    eggNOGiCOG3253, Bacteria
    HOGENOMiCLU_063226_1_0_9
    KOiK00435
    OMAiRYTMWSV
    PhylomeDBiQ8Y5F1

    Enzyme and pathway databases

    UniPathwayiUPA00252
    BioCyciLMON169963:LMO2113-MONOMER

    Family and domain databases

    HAMAPiMF_01442, Coproheme_decarbox_1, 1 hit
    InterProiView protein in InterPro
    IPR011008, Dimeric_a/b-barrel
    IPR010644, Put_peroxidase/dismutase
    IPR031332, UPF0447
    PANTHERiPTHR36843, PTHR36843, 1 hit
    PfamiView protein in Pfam
    PF06778, Chlor_dismutase, 1 hit
    SUPFAMiSSF54909, SSF54909, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiCHDC_LISMO
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q8Y5F1
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 10, 2007
    Last sequence update: March 1, 2002
    Last modified: August 12, 2020
    This is version 89 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries
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